Initial chemical approaches to the production of libraries by conventional techniques may be led by a random approach to structure design, computational chemistry and predictive modeling, analogue design based on compounds with known structure and activity, medicinal chemistry intuition, or combinations of these approaches. The libraries of compounds so produced are then screened for activity against targets of interest.
The use of combinatorial chemistry to accelerate the identification of new chemical entities with desirable properties is well established. For example, in drug discovery, large collections of compounds are often synthesized very quickly using techniques collectively called “combinatorial chemistry.” These techniques can include the parallel synthesis of compound libraries using automated and non-automated methods, and may employ both solution phase and solid phase chemistry. Such libraries may be collections of discrete, individual compounds or may consist of collections of mixed or pooled compounds, which are then screened against a target of interest. Pharmaceutically useful properties may be identified through a basic screen developed to assay the ability of compounds to bind to a molecular target. If mixtures of compounds are screened, a deconvolution process is often necessary to identify the components of a mixture that are responsible for any observed activity in the screening process. This can prove difficult to achieve in practice.
Scientists must sift through enormous numbers of potential drug candidates in their search for a single, effective drug. In many ways such high throughput screening processes have not effectively accelerated identification of new chemical entities with desirable properties.
Fragment-based drug discovery has received significant industry attention since Fesik and co-workers demonstrated that high-affinity ligands could be generated by first identifying and then combining small fragments that bound to adjacent sites on a target protein. Shuker, S. B., et al., Science 274, 1531-1534 (1996); Petros, A. M., et al., J. Med. Chem. 49, 656-663 (2006); Hajduk, P. J., et al., J. Am. Chem. Soc. 119, 5818-5827 (1997). Lead generation by fragment assembly offers an attractive complement to traditional screening: small fragments are less likely to contain interfering groups that could block an otherwise productive binding interaction, and combining prequalified fragments greatly simplifies the combinatorial search problem. Although productive techniques have been developed to identify and optimize individual fragments, the goal of merging two or more fragments to generate high-affinity compounds remains a significant challenge due to the difficulty of identifying suitable linking moieties. Erlanson, D. A., et al., J. Med. Chem. 47, 3463-3482 (2004); Jahnke, W. & Erlanson, D. A. (eds.) Fragment-based approaches in drug discovery (Wiley-VCH, Weinheim, Germany, 2006). This challenge is particularly daunting when a protein target is not amenable to structural studies, illustrating the need for simple empirical solutions to the linking problem. Tethering® with Extenders provides one such solution in which a given site on a protein is occupied by a covalently attached extender and disulfide capture is used to identify companion fragments that bind to an adjacent site. Erlanson, D. A., et al., Nat. Biotechnol. 21, 308-314. (2003); Choong, I. C., et al., J. Med. Chem. 45, 5005-5022 (2002). Initially validated using protease targets, Tethering with Extenders has recently been used to identify highly selective inhibitors of protein kinases by targeting an adaptive site adjacent to the “hinge region”. However, the high investment in protein engineering and production required to support structure-based methods or Tethering with Extenders can limit the extent to which these approaches can be routinely used.
Although such fragment-based methods have proven their utility in the development of lead candidates for medicinal chemistry optimization, there remains a need for simple, inexpensive, fast, and efficient generation of pharmacophore hits that have structures amenable to medicinal chemistry and that demonstrate affinity for or activity against biological targets of interest.